You have to create a startup script. Look in System/StartUpItems/ (not in X so it may be named slightly differently) and copy one of those folders to your user directory. Edit the files in this folder (start up item folder) so that they start the CLI app you want to start and then create a folder in your USERNAME/Library/ directory called StartUpItems/ (again I'm not in X at the moment so you need to check the name) and place the folder (start up item folder) in there.
Hope this makes since. This not for the faint hearted.
I've been using the login feature where I drop the apps in the window and it works. Then suddenly it will reset the preferences and either one, several or all apps will be removed. Im finding more bugs in this OS then positive things. And besides everything is just harder to do and takes more steps. apple has a very very long way to go.